Comparison of genetic characteristics between captive and wild giant pandas based on 13 mitochondrial coding genes.

BACKGROUND: Research on genetic diversity based on mitochondrial DNA of giant pandas mainly focused on a single marker or a few genes. OBJECTIVE: To provide a more comprehensive assessment of the genetic diversity on giant pandas based on 13 mitochondrial protein coding genes. METHODS: We assembled 13 protein coding genes in the mitochondrial genome of the giant panda based on the whole genome sequencing data, including ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6 and Cyt b. RESULTS: We successfully obtained long sequence of 11,416 base pairs with all 13 genes for 110 giant panda individual, accounting for 67.93% in length of the mitochondrial reference genome. Haplotype diversity was 0.9518 ± 0.009 and nucleotide diversity (π) was 0.00157 ± 0.00014. We detected three new haplotypes, including GPC10 and GPC21 for the CR sequence and GPB12 for the Cyt b gene. CONCLUSION: These multi-gene sequences provided more genetic variable information to compare captive and wild giant panda population.

Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda.

Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve.

The giant panda is an example of a species that has faced extensive historical habitat fragmentation, and anthropogenic disturbance and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health, and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Nonspatial and spatial capture-recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153-175 and 115-163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with four giant panda road-crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution pose a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta-population in both Wolong and throughout their current range.

Diagnosing Zygosity in Giant Panda Twins Using Short Tandem Repeats.

The giant panda, native to mountains of south-west China, is one of the world's rarest bear species and is subject to considerable conservation effort. In captivity, the proportion of twins accounts for 54% of the total number of births. To date, little is known about zygosity in panda populations - specifically, the proportion of monozygotic and dizygotic twins. In this study, we used 10 microsatellite markers for reliable zygosity testing, and the probability of monozygotic twins was 99.963% when all 10 markers were concordant. Out of 43 studied twin pairs, no MZ twins were found, indicating that there may be no identical panda twins (or the incidence is very low). We speculate that the fertilized eggs of giant pandas do not have the capability to split into two identical embryos, or that this ability is very poor, which is likely due to delayed implantation that is common in bear species. The results of this study deepen our understanding of giant panda breeding, yield insight into panda twins' likely mechanism of formation, and reduce the uncertainty of individual identity in wild population surveys.

The tomato DWD motif-containing protein DDI1 interacts with the CUL4-DDB1-based ubiquitin ligase and plays a pivotal role in abiotic stress responses.

CULLIN4(CUL4)-DAMAGED DNA BINDING PROTEIN1 (DDB1)-based ubiquitin ligase plays significant roles in multiple physiological processes via ubiquitination-mediated degradation of relevant target proteins. The DDB1-CUL4-associated factor (DCAF) acts as substrate receptor in the CUL4-DDB1 ubiquitin ligase complex and determines substrate specificity. In this study, we identified a tomato (Solanum lycopersicum) DDB1-interacting (DDI1) protein as a DCAF protein involved in response to abiotic stresses, including UV radiation, high salinity and osmotic stress. Co-immunoprecipitation and bimolecular fluorescence complementation assay indicated that DDI1 associates with CUL4-DDB1 in the nucleus. Quantitative RT-PCR analysis indicated the DDI1 gene is induced by salt, mannitol and UV-C treatment. Moreover, transgenic tomato plants with overexpression or knockdown of the DDI1 gene exhibited enhanced or attenuated tolerance to salt/mannitol/UV-C, respectively. Thus, our data suggest that DDI1 functions as a substrate receptor of the CUL4-DDB1 ubiquitin ligase, positively regulating abiotic stress response in tomato.